Need help with diagnostic please

Hey guys I was wondering if anyone could help me out here, I just bought a 06 Honda civic ex 5 spd. And what happens is when I first take off in 1st gear and get under acceleration just a little bit it grinds the gears pretty loud and that's me in 1st gear no clutch in, and it shifts perfect no slips etc, and drives fine on inter state etc and pulls good, also feels like the throwout bearing or the input shaft bearing makes noise when I'm idling but goes away with clutch pressed in, thanks for the help